Hi All,
I’ve been trying to find a web-based resource for identifying potential transcription factor binding sites in the promoters of a list of genes from
a RNAseq experiment. I’m looking for a way to input a list of gene names and then get a list of transcription factors whose predicted binding
sites are enriched in the promoters of those genes.
It seems that many tools are optimized for analyzing only one promoter at a time or that they don’t have information
on C. elegans promoters. I’ve played with Opossum, but it only searches for binding sites for a handful of worm transcription factors. Genomatix
doesn’t seem to be able to produce a list of enriched transcription factor binding sites. I know that TRANSFAC is widely used, but, again, I’m not
sure how well it would handle a large list of genes.
Can anyone recommend another resource that’s designed to perform the type of analysis that I’m looking for?
Many thanks!